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JASMINE-Mission/jasmine-imagesim

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bin/mkimage.py

Summary

Maintainability
C
1 day
Test Coverage

Avoid deeply nested control flow statements.
Open

                if varsw:
                    pixar = add_varability(pixar, injlc_iplate)

            #pixar = add_dark_current(control_params, detector, pixar)
            integrated = integrate(pixar, x0_global, y0_global,
Severity: Major
Found in bin/mkimage.py - About 45 mins to fix

    Remove this commented out code.
    Open

                #pixar = add_dark_current(control_params, detector, pixar)
    Severity: Major
    Found in bin/mkimage.py by sonar-python

    Programmers should not comment out code as it bloats programs and reduces readability.

    Unused code should be deleted and can be retrieved from source control history if required.

    See

    • MISRA C:2004, 2.4 - Sections of code should not be "commented out".
    • MISRA C++:2008, 2-7-2 - Sections of code shall not be "commented out" using C-style comments.
    • MISRA C++:2008, 2-7-3 - Sections of code should not be "commented out" using C++ comments.
    • MISRA C:2012, Dir. 4.4 - Sections of code should not be "commented out"

    Merge this if statement with the enclosing one.
    Open

                    if varsw:
    Severity: Major
    Found in bin/mkimage.py by sonar-python

    Merging collapsible if statements increases the code's readability.

    Noncompliant Code Example

    if condition1:
    if condition2:
        # ...

    Compliant Solution

    if condition1 and condition2:
    # ...

    Identical blocks of code found in 2 locations. Consider refactoring.
    Open

                if control_params.effect.wfe != 'fringe37':
                psfin = psf
                psfcenter = (np.array(np.shape(psfin))-1.0)*0.5
            else:
                psfin = psf[i_star]
    Severity: Major
    Found in bin/mkimage.py and 1 other location - About 5 hrs to fix
    bin/galcenimg.py on lines 145..150

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 95.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    Identical blocks of code found in 2 locations. Consider refactoring.
    Open

                pixcube_global[x0_global:x0_global+Npixcube,
                    y0_global:y0_global+Npixcube, iplate] +=\
                pixcube[:, :, iplate]
    Severity: Major
    Found in bin/mkimage.py and 1 other location - About 1 hr to fix
    bin/galcenimg.py on lines 173..174

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 47.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    Identical blocks of code found in 2 locations. Consider refactoring.
    Open

        if control_params.effect.ace == 'gauss':
        psf = apply_gaussian(psf, control_params.ace_control['acex_std'],\
                             control_params.ace_control['acey_std'], fp_scale)
    Severity: Major
    Found in bin/mkimage.py and 1 other location - About 1 hr to fix
    bin/galcenimg.py on lines 109..111

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 42.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    Identical blocks of code found in 2 locations. Consider refactoring.
    Open

            if args['--var']:
            varsw, injlc, b = variability.read_var(tday, line['star index'])
    Severity: Minor
    Found in bin/mkimage.py and 1 other location - About 30 mins to fix
    bin/mkimage_nosub.py on lines 312..313

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 32.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    Line too long (214 > 79 characters)
    Open

    from jis.binutils.runpixsim import init_pix, uniform_flat, init_images, set_positions, make_local_flat, index_control_trajectory, calc_theta, scaling_pixar, add_varability, add_dark_current, run_simpix, global_dark
    Severity: Minor
    Found in bin/mkimage.py by pep8

    Limit all lines to a maximum of 79 characters.

    There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

    Line too long (80 > 79 characters)
    Open

       --det det.json              json file containing detector related parameters.
    Severity: Minor
    Found in bin/mkimage.py by pep8

    Limit all lines to a maximum of 79 characters.

    There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

    Line too long (217 > 79 characters)
    Open

        mkimage.py [-h|--help] [--pd paramdir] --starplate star_plate.csv [--var variability.json] --det det.json --tel tel.json --ace ace.json --ctl ctl.json [--dft drift.json] --format format [--od outdir] [--overwrite]
    Severity: Minor
    Found in bin/mkimage.py by pep8

    Limit all lines to a maximum of 79 characters.

    There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

    Line too long (82 > 79 characters)
    Open

        acex, acey, Nts_per_plate = run_calc_ace(control_params, detector, ace_params)
    Severity: Minor
    Found in bin/mkimage.py by pep8

    Limit all lines to a maximum of 79 characters.

    There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

    At least two spaces before inline comment
    Open

        pixcube_global += gd # add dark.
    Severity: Minor
    Found in bin/mkimage.py by pep8

    Separate inline comments by at least two spaces.

    An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

    Line too long (88 > 79 characters)
    Open

       --format format             format of the output file (platefits, fitscube, hdfcube).
    Severity: Minor
    Found in bin/mkimage.py by pep8

    Limit all lines to a maximum of 79 characters.

    There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

    Line too long (211 > 79 characters)
    Open

            Curretly, the time resolution should be prepared in the unit of control_params.tplate + detector.readparams.t_scan. We do not support the finest time resolution yet (control_params.ace_control['dtace']).
    Severity: Minor
    Found in bin/mkimage.py by pep8

    Limit all lines to a maximum of 79 characters.

    There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

    Line too long (313 > 79 characters)
    Open

            In the process to make pixar, Nts_per_plate is multiplied to the result of simpix to make the units of pixar to be e/pix/control_params.ace_control['dtace']. But, in none/gauss mode, the scaling is not correct for simulating a single-shot image. Therefore, we divide pixar by Nts_per_plate for correction.
    Severity: Minor
    Found in bin/mkimage.py by pep8

    Limit all lines to a maximum of 79 characters.

    There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

    Line too long (87 > 79 characters)
    Open

        table_starplate, detector, control_params, telescope, ace_params = load_parameters(
    Severity: Minor
    Found in bin/mkimage.py by pep8

    Limit all lines to a maximum of 79 characters.

    There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

    Unexpected indentation (comment)
    Open

            # acex and acey are normalized with their stddevs.
    Severity: Minor
    Found in bin/mkimage.py by pep8

    Use indent_size (PEP8 says 4) spaces per indentation level.

    For really old code that you don't want to mess up, you can continue
to use 8-space tabs.

Okay: a = 1
Okay: if a == 0:\n    a = 1
E111:   a = 1
E114:   # a = 1

Okay: for item in items:\n    pass
E112: for item in items:\npass
E115: for item in items:\n# Hi\n    pass

Okay: a = 1\nb = 2
E113: a = 1\n    b = 2
E116: a = 1\n    # b = 2

    The backslash is redundant between brackets
    Open

            psf = apply_gaussian(psf, control_params.ace_control['acex_std'],\
    Severity: Minor
    Found in bin/mkimage.py by pep8

    Avoid explicit line join between brackets.

    The preferred way of wrapping long lines is by using Python's
implied line continuation inside parentheses, brackets and braces.
Long lines can be broken over multiple lines by wrapping expressions
in parentheses.  These should be used in preference to using a
backslash for line continuation.

E502: aaa = [123, \\n       123]
E502: aaa = ("bbb " \\n       "ccc")

Okay: aaa = [123,\n       123]
Okay: aaa = ("bbb "\n       "ccc")
Okay: aaa = "bbb " \\n    "ccc"
Okay: aaa = 123  # \\

    At least two spaces before inline comment
    Open

                np.sqrt(2.)*detector.readnoise)[0] # add noise.
    Severity: Minor
    Found in bin/mkimage.py by pep8

    Separate inline comments by at least two spaces.

    An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

    Line too long (80 > 79 characters)
    Open

       --pd paramdir               name of the directory containing parameter files.
    Severity: Minor
    Found in bin/mkimage.py by pep8

    Limit all lines to a maximum of 79 characters.

    There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

    Line too long (147 > 79 characters)
    Open

       --var variability.json      json file for stellar variability/transit (optional). The input variability will be shown in variability_input().png
    Severity: Minor
    Found in bin/mkimage.py by pep8

    Limit all lines to a maximum of 79 characters.

    There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

    Line too long (85 > 79 characters)
    Open

            filenames, control_params, detector, acex, acey, detpix_scale, args['--dft'])
    Severity: Minor
    Found in bin/mkimage.py by pep8

    Limit all lines to a maximum of 79 characters.

    There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

    Line too long (81 > 79 characters)
    Open

       --tel tel.json              json file containing telescope related parameters.
    Severity: Minor
    Found in bin/mkimage.py by pep8

    Limit all lines to a maximum of 79 characters.

    There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

    Line too long (98 > 79 characters)
    Open

            # Making a cube containing plate data for a local region (small frame for a local region).
    Severity: Minor
    Found in bin/mkimage.py by pep8

    Limit all lines to a maximum of 79 characters.

    There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

    Line too long (94 > 79 characters)
    Open

    from jis.binutils.runphotonsim import run_calc_wfe, run_calc_psf, run_calc_ace, apply_gaussian
    Severity: Minor
    Found in bin/mkimage.py by pep8

    Limit all lines to a maximum of 79 characters.

    There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

    Line too long (125 > 79 characters)
    Open

       --starplate star_plate.csv  csv file containing star info (plate index, star index, x pixel, y pixel, lambda, beta, Hwmag)
    Severity: Minor
    Found in bin/mkimage.py by pep8

    Limit all lines to a maximum of 79 characters.

    There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

    Line too long (87 > 79 characters)
    Open

            xc_local, yc_local, x0_global, y0_global, xc_global, yc_global = set_positions(
    Severity: Minor
    Found in bin/mkimage.py by pep8

    Limit all lines to a maximum of 79 characters.

    There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

    Block comment should start with '# '
    Open

                #pixar = add_dark_current(control_params, detector, pixar)
    Severity: Minor
    Found in bin/mkimage.py by pep8

    Separate inline comments by at least two spaces.

    An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

    At least two spaces before inline comment
    Open

        pixcube_global = np.round(pixcube_global/detector.gain) # digitize.
    Severity: Minor
    Found in bin/mkimage.py by pep8

    Separate inline comments by at least two spaces.

    An inline comment is a comment on the same line as a statement.
Inline comments should be separated by at least two spaces from the
statement. They should start with a # and a single space.

Each line of a block comment starts with a # and a single space
(unless it is indented text inside the comment).

Okay: x = x + 1  # Increment x
Okay: x = x + 1    # Increment x
Okay: # Block comment
E261: x = x + 1 # Increment x
E262: x = x + 1  #Increment x
E262: x = x + 1  #  Increment x
E265: #Block comment
E266: ### Block comment

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